1,577 research outputs found
Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations
Common algorithms for computationally simulating Langevin dynamics must
discretize the stochastic differential equations of motion. These resulting
finite time step integrators necessarily have several practical issues in
common: Microscopic reversibility is violated, the sampled stationary
distribution differs from the desired equilibrium distribution, and the work
accumulated in nonequilibrium simulations is not directly usable in estimators
based on nonequilibrium work theorems. Here, we show that even with a
time-independent Hamiltonian, finite time step Langevin integrators can be
thought of as a driven, nonequilibrium physical process. Once an appropriate
work-like quantity is defined -- here called the shadow work -- recently
developed nonequilibrium fluctuation theorems can be used to measure or correct
for the errors introduced by the use of finite time steps. In particular, we
demonstrate that amending estimators based on nonequilibrium work theorems to
include this shadow work removes the time step dependent error from estimates
of free energies. We also quantify, for the first time, the magnitude of
deviations between the sampled stationary distribution and the desired
equilibrium distribution for equilibrium Langevin simulations of solvated
systems of varying size. While these deviations can be large, they can be
eliminated altogether by Metropolization or greatly diminished by small
reductions in the time step. Through this connection with driven processes,
further developments in nonequilibrium fluctuation theorems can provide
additional analytical tools for dealing with errors in finite time step
integrators.Comment: 11 pages, 4 figure
Adaptive multi-stage integrators for optimal energy conservation in molecular simulations
We introduce a new Adaptive Integration Approach (AIA) to be used in a wide
range of molecular simulations. Given a simulation problem and a step size, the
method automatically chooses the optimal scheme out of an available family of
numerical integrators. Although we focus on two-stage splitting integrators,
the idea may be used with more general families. In each instance, the
system-specific integrating scheme identified by our approach is optimal in the
sense that it provides the best conservation of energy for harmonic forces. The
AIA method has been implemented in the BCAM-modified GROMACS software package.
Numerical tests in molecular dynamics and hybrid Monte Carlo simulations of
constrained and unconstrained physical systems show that the method
successfully realises the fail-safe strategy. In all experiments, and for each
of the criteria employed, the AIA is at least as good as, and often
significantly outperforms the standard Verlet scheme, as well as fixed
parameter, optimized two-stage integrators. In particular, the sampling
efficiency found in simulations using the AIA is up to 5 times better than the
one achieved with other tested schemes
Numerical implementation of the exact dynamics of free rigid bodies
In this paper the exact analytical solution of the motion of a rigid body
with arbitrary mass distribution is derived in the absence of forces or
torques. The resulting expressions are cast into a form where the dependence of
the motion on initial conditions is explicit and the equations governing the
orientation of the body involve only real numbers. Based on these results, an
efficient method to calculate the location and orientation of the rigid body at
arbitrary times is presented. This implementation can be used to verify the
accuracy of numerical integration schemes for rigid bodies, to serve as a
building block for event-driven discontinuous molecular dynamics simulations of
general rigid bodies, and for constructing symplectic integrators for rigid
body dynamics.Comment: Shortened paper with updated references, 28 pages, 3 figure
Palindromic 3-stage splitting integrators, a roadmap
The implementation of multi-stage splitting integrators is essentially the
same as the implementation of the familiar Strang/Verlet method. Therefore
multi-stage formulas may be easily incorporated into software that now uses the
Strang/Verlet integrator. We study in detail the two-parameter family of
palindromic, three-stage splitting formulas and identify choices of parameters
that may outperform the Strang/Verlet method. One of these choices leads to a
method of effective order four suitable to integrate in time some partial
differential equations. Other choices may be seen as perturbations of the
Strang method that increase efficiency in molecular dynamics simulations and in
Hybrid Monte Carlo sampling.Comment: 20 pages, 8 figures, 2 table
Optimized Verlet-like algorithms for molecular dynamics simulations
New explicit velocity- and position-Verlet-like algorithms of the second
order are proposed to integrate the equations of motion in many-body systems.
The algorithms are derived on the basis of an extended decomposition scheme at
the presence of a free parameter. The nonzero value for this parameter is
obtained by reducing the influence of truncated terms to a minimum. As a
result, the new algorithms appear to be more efficient than the original Verlet
versions which correspond to a particular case when the introduced parameter is
equal to zero. Like the original versions, the proposed counterparts are
symplectic and time reversible, but lead to an improved accuracy in the
generated solutions at the same overall computational costs. The advantages of
the new algorithms are demonstrated in molecular dynamics simulations of a
Lennard-Jones fluid.Comment: 5 pages, 2 figures; submitted to Phys. Rev.
Efficient algorithms for rigid body integration using optimized splitting methods and exact free rotational motion
Hamiltonian splitting methods are an established technique to derive stable
and accurate integration schemes in molecular dynamics, in which additional
accuracy can be gained using force gradients. For rigid bodies, a tradition
exists in the literature to further split up the kinetic part of the
Hamiltonian, which lowers the accuracy. The goal of this note is to comment on
the best combination of optimized splitting and gradient methods that avoids
splitting the kinetic energy. These schemes are generally applicable, but the
optimal scheme depends on the desired level of accuracy. For simulations of
liquid water it is found that the velocity Verlet scheme is only optimal for
crude simulations with accuracies larger than 1.5%, while surprisingly a
modified Verlet scheme (HOA) is optimal up to accuracies of 0.4% and a fourth
order gradient scheme (GIER4) is optimal for even higher accuracies.Comment: 2 pages, 1 figure. Added clarifying comments. Accepted for
publication in the Journal of Chemical Physic
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